Intrinsically-disordered N-termini in human parechovirus 1 capsid proteins bind encapsidated RNA

Shabih Shakeel,C Cheng Kao,Robert C Vaughan,James D Evans,Sarah J Butcher,Mark Hazelbaker

doi:10.1038/s41598-018-23552-7

Abstract

Human parechoviruses (HPeV) are picornaviruses with a highly-ordered RNA genome contained within icosahedrally-symmetric capsids. Ordered RNA structures have recently been shown to interact with capsid proteins VP1 and VP3 and facilitate virus assembly in HPeV1. Using an assay that combines reversible cross-linking, RNA affinity purification and peptide mass fingerprinting (RCAP), we mapped the RNA-interacting regions of the capsid proteins from the whole HPeV1 virion in solution. The intrinsically-disordered N-termini of capsid proteins VP1 and VP3, and unexpectedly, VP0, were identified to interact with RNA. Comparing these results to those obtained using recombinantly-expressed VP0 and VP1 confirmed the virion binding regions, and revealed unique RNA binding regions in the isolated VP0 not previously observed in the crystal structure of HPeV1. We used RNA fluorescence anisotropy to confirm the RNA-binding competency of each of the capsid proteins’ N-termini. These findings suggests that dynamic interactions between the viral RNA and the capsid proteins modulate virus assembly, and suggest a novel role for VP0.

Highlights

Human parechoviruses (HPeV) are important human pathogens for which we lack antivirals or vaccines
Regions of structured RNA were recently identified as packaging signals (PSs) that interact with VP1 and VP3 in the HPeV virion[4]
RCAP analysis on whole HPeV1 virions identified that several sequences from VP0, VP1 and VP3 contacted the encapsidated RNA (Table 1; Fig. 1; Supplementary Figure 1)

Summary

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VP1 protein were shown to bind both the full genome as well as several sub-genome length RNAs. Curiously, the RNA binding profile of VP0 differed dramatically when analyzed in the context of the virion or with the recombinant VP0. RNA fluorescence anisotropy was used to confirm that the disordered capsid N-termini contact the genome. We propose that these highly disordered regions are important for both RNA binding and the co-assembly of the virion genome and capsid proteins

Results and Discussion

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Amino acid sequencea

Methods

Additional Information